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  1. IGB
  2. IGBF-2274

Create genome dashboard showing genome pictures for quickly going to a genome

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Story Points:
      2
    • Sprint:
      Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May

      Description

      Let's create a single page app (or even simpler) that shows images representing genomes.

      When a user clicks on an image, IGB (if it is running) will load the genome.

      See:

      https://wiki.transvar.org/display/igbman/Controlling+IGB+using+IGB+Links

      Example link:

      http://localhost:7085/UnibrowControl?version=A_thaliana_Jun_2009

      Valid versions are available in the first first column from:
      http://igbquickload.org/quickload/contents.txt

      Please add to the BioViz code base.

      Note that if you want to use other versions of javascript or bootstrap libraries than are used elsewhere on the site, that's fine.

      Also, more than one person is welcome to work on this.

      Karthik Raveendran
      Sameer Shanbhag

        Attachments

          Activity

          Hide
          aloraine Ann Loraine added a comment - - edited

          Change requests:

          • http://quickload.bioviz.org/quickload/contents.txt' - why use this instead of contents.txt from the main igbquickload site – igbquickload.org/quickload/contents.txt? They are supposed to be mirrors of each other, but quickload.bioviz.org is the backup site for igquickload.org. Please use igbquickloard.org instead.
          • The main quickload site often changes. I add new species and genome assemblies frequently. The genome dashboard code needs to be able to handle this. What happens if a genome and species show up that don't have an image?
          • Is it possible to get the images directly from the IGB code base? The names of the files all follow the same pattern, so you could link to them some of them from the dashboard.

          As an example, here is the path to Arabidopsis lyrata:

          https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/core/common/src/main/resources/images/A_lyrata.png

          Show
          aloraine Ann Loraine added a comment - - edited Change requests: utility/util.js uses this URL: https://wiki.transvar.org/download/attachments/19955940/species.txt?api=v2 ' It is extremely likely this link will break. Instead, link to synonyms.txt which is version controlled and maintained in the IGB code base itself. http://quickload.bioviz.org/quickload/contents.txt ' - why use this instead of contents.txt from the main igbquickload site – igbquickload.org/quickload/contents.txt? They are supposed to be mirrors of each other, but quickload.bioviz.org is the backup site for igquickload.org. Please use igbquickloard.org instead. The main quickload site often changes. I add new species and genome assemblies frequently. The genome dashboard code needs to be able to handle this. What happens if a genome and species show up that don't have an image? Is it possible to get the images directly from the IGB code base? The names of the files all follow the same pattern, so you could link to them some of them from the dashboard. As an example, here is the path to Arabidopsis lyrata: https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/core/common/src/main/resources/images/A_lyrata.png
          Hide
          aloraine Ann Loraine added a comment -

          A question:

          • Also, can the dashboard allow use of png format files instead of jpg? It would be nice if this were somewhat flexible to allow images of any format.
          Show
          aloraine Ann Loraine added a comment - A question: Also, can the dashboard allow use of png format files instead of jpg? It would be nice if this were somewhat flexible to allow images of any format.
          Hide
          sameer Sameer Shanbhag (Inactive) added a comment -

          Changelog:

          • Updated all the links to use IGB Codebase for Species and Synonyms file.
          • Update contents.txt tile URL from quickload.bioviz.org to igbquickload.org

          Regarding Images:

          • We can get the images from IGB codebase, but I am not sure how the images will look with our design. I can try doing that if required.

          Changes can be found:

          Show
          sameer Sameer Shanbhag (Inactive) added a comment - Changelog: Updated all the links to use IGB Codebase for Species and Synonyms file. Update contents.txt tile URL from quickload.bioviz.org to igbquickload.org Regarding Images: We can get the images from IGB codebase, but I am not sure how the images will look with our design. I can try doing that if required. Changes can be found: https://bitbucket.org/sshanbh1/genome-dashboard/commits/1871339abfddd9cae7009c4316d4726821b64c52
          Hide
          aloraine Ann Loraine added a comment -

          The above URLs are good.
          Regarding images: Please stick with the current images if they look better than corresponding images in IGB itself. On second thought, since this an entirely different application with its own look, we should not blindly use the images in the git repository.

          Show
          aloraine Ann Loraine added a comment - The above URLs are good. Regarding images: Please stick with the current images if they look better than corresponding images in IGB itself. On second thought, since this an entirely different application with its own look, we should not blindly use the images in the git repository.
          Hide
          sameer Sameer Shanbhag (Inactive) added a comment -

          Change Log:

          • Implemented a dynamic approach for images.

          Requirement:

          • Image file must start with a common name eg. A_gambiae

          Changes can be found at:

          Show
          sameer Sameer Shanbhag (Inactive) added a comment - Change Log: Implemented a dynamic approach for images. Requirement: Image file must start with a common name eg. A_gambiae Changes can be found at: https://bitbucket.org/sshanbh1/genome-dashboard/commits/8145e77c141eedae4ee23a24a9ac9812cb8c1fe2

            People

            • Assignee:
              sameer Sameer Shanbhag (Inactive)
              Reporter:
              aloraine Ann Loraine
            • Votes:
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              Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: